利用全基因组测序技术研究埃塞俄比亚阿姆哈拉地区耐多药结核分枝杆菌菌株的分子流行病学和传播动态。
Molecular epidemiology and transmission dynamics of multi-drug resistant tuberculosis strains using whole genome sequencing in the Amhara region, Ethiopia.
机构信息
Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia.
Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA.
出版信息
BMC Genomics. 2023 Jul 17;24(1):400. doi: 10.1186/s12864-023-09502-2.
BACKGROUND
Drug resistant Mycobacterium tuberculosis prevention and care is a major challenge in Ethiopia. The World health organization has designated Ethiopia as one of the 30 high burden multi-drug resistant tuberculosis (MDR-TB) countries. There is limited information regarding genetic diversity and transmission dynamics of MDR-TB in Ethiopia.
OBJECTIVE
To investigate the molecular epidemiology and transmission dynamics of MDR-TB strains using whole genome sequence (WGS) in the Amhara region.
METHODS
Forty-five MDR-TB clinical isolates from Amhara region were collected between 2016 and 2018, and characterized using WGS and 24-loci Mycobacterium Interspersed Repetitive Units Variable Number of Tandem Repeats (MIRU-VNTR) typing. Clusters were defined based on the maximum distance of 12 single nucleotide polymorphisms (SNPs) or alleles as the upper threshold of genomic relatedness. Five or less SNPs or alleles distance or identical 24-loci VNTR typing is denoted as surrogate marker for recent transmission.
RESULTS
Forty-one of the 45 isolates were analyzed by WGS and 44% (18/41) of the isolates were distributed into 4 clusters. Of the 41 MDR-TB isolates, 58.5% were classified as lineage 4, 36.5% lineage 3 and 5% lineage 1. Overall, TUR genotype (54%) was the predominant in MDR-TB strains. 41% (17/41) of the isolates were clustered into four WGS groups and the remaining isolates were unique strains. The predominant cluster (Cluster 1) was composed of nine isolates belonging to lineage 4 and of these, four isolates were in the recent transmission links.
CONCLUSIONS
Majority of MDR-TB strain cluster and predominance of TUR lineage in the Amhara region give rise to concerns for possible ongoing transmission. Efforts to strengthen TB laboratory to advance diagnosis, intensified active case finding, and expanded contact tracing activities are needed in order to improve rapid diagnosis and initiate early treatment. This would lead to the interruption of the transmission chain and stop the spread of MDR-TB in the Amhara region.
背景
在埃塞俄比亚，耐药结核分枝杆菌的预防和护理是一个主要挑战。世界卫生组织已将埃塞俄比亚列为 30 个高负担耐多药结核（MDR-TB）国家之一。关于埃塞俄比亚 MDR-TB 的遗传多样性和传播动力学，信息有限。
目的
使用全基因组序列（WGS）在阿姆哈拉地区调查 MDR-TB 菌株的分子流行病学和传播动态。
方法
2016 年至 2018 年期间收集了来自阿姆哈拉地区的 45 株 MDR-TB 临床分离株，并使用 WGS 和 24 个位点分枝杆菌散布重复单位可变数串联重复（MIRU-VNTR）分型进行了特征描述。聚类是基于最大距离为 12 个单核苷酸多态性（SNP）或等位基因作为基因组相关性的上限来定义的。距离为 5 个或更少的 SNP 或等位基因或相同的 24 个位点 VNTR 分型表示最近的传播替代标志物。
结果
对 45 株分离株中的 41 株进行了 WGS 分析，其中 44%（18/41）的分离株分布在 4 个聚类中。在 41 株 MDR-TB 分离株中，58.5%为 4 谱系，36.5%为 3 谱系，5%为 1 谱系。总体而言，TUR 基因型（54%）是 MDR-TB 菌株中的主要基因型。41%（17/41）的分离株聚类为 4 个 WGS 组，其余分离株为独特株。主要聚类（聚类 1）由 9 株属于 4 谱系的分离株组成，其中 4 株处于近期传播链中。
结论
阿姆哈拉地区 MDR-TB 菌株的大多数集群和 TUR 谱系的优势引起了对可能正在进行的传播的关注。需要加强结核病实验室以推进诊断，强化主动病例发现，并扩大接触者追踪活动，以便改善快速诊断并尽早开始治疗。这将导致传播链的中断，并阻止 MDR-TB 在阿姆哈拉地区的传播。
Zotero 插件